hostname can't be null error

Andrew Skol

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Sep 11, 2019, 3:00:29 PM9/11/19

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Hi Folks,

I recently installed IGV 2.6.3 from the "IGV for Windows" file on a Windows 10 machine. After clicking on start icon a window would appear and disappear rapidly and IGV would never start. After a little exploring, I changed the igv.bat script so that java was invoked instead of javaw, which allowed me to capture the error below. Interestingly, I had installed 2.6.2 a couple of days ago and it was working (with a few network issues (couldn't access genome or annotation files from the server) which is probably internal). I then uninstalled it to install version 2.6.3 and ran into this issue. I was unable to run 2.6.2 after I reinstalled it. Any help would be greatly appreciated.

Best,

Andrew

openjdk version "11.0.2" 2019-01-15

OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.2+9)

OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.2+9, mixed mode)

WARN [2019-09-11T13:47:19,864] [Globals.java:138] [AWT-EventQueue-0] Development mode is enabled

INFO [2019-09-11T13:47:19,904] [DirectoryManager.java:84] [AWT-EventQueue-0] Fetching user directory...

INFO [2019-09-11T13:47:19,940] [DirectoryManager.java:179] [AWT-EventQueue-0] IGV Directory: C:\Users\askol\igv

INFO [2019-09-11T13:47:19,953] [Main.java:156] [AWT-EventQueue-0] Startup IGV Version 2.6.3 08/27/2019 12:03 AM

INFO [2019-09-11T13:47:19,961] [Main.java:157] [AWT-EventQueue-0] Java 11.0.2 (build 11.0.2+9) 2019-01-15

INFO [2019-09-11T13:47:19,962] [Main.java:160] [AWT-EventQueue-0] Java Vendor: AdoptOpenJDK https://adoptopenjdk.net/

INFO [2019-09-11T13:47:19,962] [Main.java:162] [AWT-EventQueue-0] JVM: OpenJDK 64-Bit Server VM AdoptOpenJDK

INFO [2019-09-11T13:47:19,963] [Main.java:165] [AWT-EventQueue-0] Default User Directory: C:\Users\askol\Documents

INFO [2019-09-11T13:47:19,964] [Main.java:166] [AWT-EventQueue-0] OS: Windows 10 10.0 amd64

ERROR [2019-09-11T13:47:20,377] [DefaultExceptionHandler.java:49] [AWT-EventQueue-0] Unhandled exception

java.lang.IllegalArgumentException: hostname can't be null

at java.net.InetSocketAddress.checkHost(Unknown Source) ~[?:?]

at java.net.InetSocketAddress.<init>(Unknown Source) ~[?:?]

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:763) ~[igv.jar:?]

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:695) ~[igv.jar:?]

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:691) ~[igv.jar:?]

at org.broad.igv.util.HttpUtils.getContentsAsGzippedString(HttpUtils.java:213) ~[igv.jar:?]

at org.broad.igv.google.OAuthUtils.fetchOauthProperties(OAuthUtils.java:110) ~[igv.jar:?]

at org.broad.igv.google.OAuthUtils.<init>(OAuthUtils.java:101) ~[igv.jar:?]

at org.broad.igv.google.OAuthUtils.getInstance(OAuthUtils.java:93) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.createGoogleMenu(IGVMenuBar.java:964) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.createMenus(IGVMenuBar.java:182) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.<init>(IGVMenuBar.java:148) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.lambda$createInstance$1(IGVMenuBar.java:135) ~[igv.jar:?]

at org.broad.igv.ui.util.UIUtilities.invokeAndWaitOnEventThread(UIUtilities.java:166) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.createInstance(IGVMenuBar.java:135) ~[igv.jar:?]

at org.broad.igv.ui.IGV.<init>(IGV.java:241) ~[igv.jar:?]

at org.broad.igv.ui.IGV.createInstance(IGV.java:142) ~[igv.jar:?]

at org.broad.igv.ui.Main.open(Main.java:294) ~[igv.jar:?]

at org.broad.igv.ui.Main$1.run(Main.java:111) ~[igv.jar:?]

at java.awt.event.InvocationEvent.dispatch(Unknown Source) ~[?:?]

at java.awt.EventQueue.dispatchEventImpl(Unknown Source) ~[?:?]

at java.awt.EventQueue$4.run(Unknown Source) ~[?:?]

at java.security.AccessController.doPrivileged(Native Method) ~[?:?]

at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) ~[?:?]

at java.awt.EventQueue.dispatchEvent(Unknown Source) ~[?:?]

at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:?]

at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:?]

at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:?]

at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:?]

at java.awt.EventDispatchThread.run(Unknown Source) [?:?]

James Robinson

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Sep 11, 2019, 3:21:47 PM9/11/19

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can you try with the snapshot version? If the error remains can you give us the stacktrace again as line numbers night have changed. https://software.broadinstitute.org/software/igv/download_snapshot

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Andrew Skol

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Sep 11, 2019, 4:47:25 PM9/11/19

to igv-help

Thanks for your quick response. The issue persists with the snapshot version. The stacktrace from this run looks like this (I simply changed javaw to java). Thanks again for your help.

openjdk version "11.0.2" 2019-01-15

OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.2+9)

OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.2+9, mixed mode)

WARN [2019-09-11T15:40:10,885] [Globals.java:139] [AWT-EventQueue-0] Development mode is enabled

INFO [2019-09-11T15:40:10,920] [DirectoryManager.java:84] [AWT-EventQueue-0] Fetching user directory...

INFO [2019-09-11T15:40:10,959] [DirectoryManager.java:179] [AWT-EventQueue-0] IGV Directory: C:\Users\askol\igv

INFO [2019-09-11T15:40:10,971] [Main.java:150] [AWT-EventQueue-0] Startup IGV Version snapshot 09/10/2019 09:16 PM

INFO [2019-09-11T15:40:10,979] [Main.java:151] [AWT-EventQueue-0] Java 11.0.2 (build 11.0.2+9) 2019-01-15

INFO [2019-09-11T15:40:10,979] [Main.java:154] [AWT-EventQueue-0] Java Vendor: AdoptOpenJDK https://adoptopenjdk.net/

INFO [2019-09-11T15:40:10,980] [Main.java:156] [AWT-EventQueue-0] JVM: OpenJDK 64-Bit Server VM AdoptOpenJDK

INFO [2019-09-11T15:40:10,981] [Main.java:159] [AWT-EventQueue-0] Default User Directory: C:\Users\askol\Documents

INFO [2019-09-11T15:40:10,982] [Main.java:160] [AWT-EventQueue-0] OS: Windows 10 10.0 amd64

ERROR [2019-09-11T15:40:11,407] [DefaultExceptionHandler.java:49] [AWT-EventQueue-0] Unhandled exception

java.lang.IllegalArgumentException: hostname can't be null

at java.net.InetSocketAddress.checkHost(Unknown Source) ~[?:?]

at java.net.InetSocketAddress.<init>(Unknown Source) ~[?:?]

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:776) ~[igv.jar:?]

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:708) ~[igv.jar:?]

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:704) ~[igv.jar:?]

at org.broad.igv.util.HttpUtils.getContentsAsGzippedString(HttpUtils.java:220) ~[igv.jar:?]

at org.broad.igv.google.OAuthUtils.fetchOauthProperties(OAuthUtils.java:129) ~[igv.jar:?]

at org.broad.igv.google.OAuthUtils.<init>(OAuthUtils.java:119) ~[igv.jar:?]

at org.broad.igv.google.OAuthUtils.getInstance(OAuthUtils.java:109) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.createGoogleMenu(IGVMenuBar.java:1059) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.createMenus(IGVMenuBar.java:185) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.<init>(IGVMenuBar.java:151) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.lambda$createInstance$1(IGVMenuBar.java:138) ~[igv.jar:?]

at org.broad.igv.ui.util.UIUtilities.invokeAndWaitOnEventThread(UIUtilities.java:166) ~[igv.jar:?]

at org.broad.igv.ui.IGVMenuBar.createInstance(IGVMenuBar.java:138) ~[igv.jar:?]

at org.broad.igv.ui.IGV.<init>(IGV.java:241) ~[igv.jar:?]

at org.broad.igv.ui.IGV.createInstance(IGV.java:142) ~[igv.jar:?]

at org.broad.igv.ui.Main.open(Main.java:288) ~[igv.jar:?]

at org.broad.igv.ui.Main.lambda$main$0(Main.java:106) ~[igv.jar:?]

at java.awt.event.InvocationEvent.dispatch(Unknown Source) ~[?:?]

at java.awt.EventQueue.dispatchEventImpl(Unknown Source) ~[?:?]

at java.awt.EventQueue$4.run(Unknown Source) ~[?:?]

at java.security.AccessController.doPrivileged(Native Method) ~[?:?]

at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) ~[?:?]

at java.awt.EventQueue.dispatchEvent(Unknown Source) ~[?:?]

at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:?]

at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:?]

at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:?]

at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:?]

at java.awt.EventDispatchThread.run(Unknown Source) [?:?]

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Helga Thorvaldsdottir

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Sep 11, 2019, 5:07:43 PM9/11/19

to igv-help

Hi Andrew,

I've seen this error message before when the "Use proxy" box is checked in the IGV preferences, but no proxy host was specified.

Can you check the prefs.properties file in the igv folder in your home directory and see if it has the entry

PROXY.USE=true

If so, either try removing that entry, or adding a line

PROXY.HOST=<your proxy host>

where <your proxy host> is replaced with the hostname of your proxy host.

Helga

Andrew Skol

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Sep 12, 2019, 10:31:03 AM9/12/19

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Bingo. Thank you so much Helga and James!

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